WASHINGTON (CNN) -- Samuel Berger, former President Clinton's national security adviser, is under federal criminal investigation for allegedly removing classified documents and handwritten notes from a National Archives screening room during preparations for his testimony before the 9/11 commission.

Sources familiar with the investigation confirmed it to CNN on Monday.

The sources told CNN the investigation began last October, after Berger spent roughly 30 hours over three or four days reviewing what one said was "tens of thousands of pages" of Clinton administration documents to comply with a request from the 9/11 commission.

Berger was designated as the official from the Clinton administration who would review documents relevant to commission inquiries. He was also a witness at the 9/11 commission hearings and reviewed records to prepare for his personal testimony.

The Associated Press first reported the story Monday.

In a statement, Berger acknowledged that he removed his handwritten notes without first having them reviewed for sensitive information, and he also said he "inadvertently" removed some of the classified documents he had reviewed during his time at the Archives.

National Archives' policy requires that if someone reviews classified documents and wants to take their handwritten notes with them, those notes must first be cleared by archivists.

In his statement, Berger said that "when I was informed by the Archives there were documents missing, I immediately returned everything I had, except for a few documents that apparently I had accidentally discarded."

"I deeply regret the sloppiness involved, but I had no intention of withholding documents from the commission, and to the contrary, to my knowledge, every document requested by the commission from the Clinton administration was produced," he said.

A Berger associate, who spoke on condition of anonymity, said the FBI served warrants and searched both Berger's home and office earlier this year as part of the investigation.

A government official familiar with the investigation said that some documents are still missing.

Among the documents Berger says he inadvertently took, the sources confirmed, were drafts of a Clinton administration "after action" report on efforts to thwart al Qaeda around the time of the millennium.

Archives officials told investigators that at least one draft of that report is still missing.

Officials close to Berger said it was ludicrous to suggest that he was trying to hide damaging information from the 9/11 commission.

They said the drafts were written by Clinton counterterrorism czar Richard Clarke and had been changed somewhat, as is customary, as the drafts were circulated among relevant agencies and officials.

But the sources close to Berger said there were other copies of the drafts, that the commission had the final version of the report and that Clarke had said there were not significant changes during the drafting process.

The sources said the FBI had contacted Berger several months ago and that he hired Lanny Breuer, who has since been in contact with prosecutors.

Berger has stressed his willingness to cooperate, but investigators have not asked to speak directly with him as yet, the sources said.

Asked if it unusual that Berger has not yet been interviewed, the government official familiar with the investigation responded that investigators would do so once they are satisfied they have the evidence they need.

Sources close to Berger said they did not believe there was a grand jury impaneled as part of the investigation and that to the best of their knowledge, Clarke and other Clinton administration officials who have knowledge of the documents in question -- and specifically about any changes made in the drafting process of the millennium report -- have not been questioned.

One of these sources questioned the timing of the leak, three days before the public release of the 9/11 commission report.

"There is a story here, and Sandy concedes he made an inadvertent mistake," one source, a former Clinton administration colleague, said. "But this has been kept confidential for months. So why now?"

A Justice Department spokesman had no comment when asked about the Berger probe.

Berger currently serves as an informal adviser to the campaign of presumptive Democratic presidential nominee Sen. John Kerry.